Gene loci information

Transcript annotation

  • This transcript has been annotated as Calmodulin.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g11432 g11432.t53 TTS g11432.t53 16197707 16197707
chr_1 g11432 g11432.t53 isoform g11432.t53 16197920 16200849
chr_1 g11432 g11432.t53 exon g11432.t53.exon1 16197920 16197948
chr_1 g11432 g11432.t53 cds g11432.t53.CDS1 16197920 16197948
chr_1 g11432 g11432.t53 exon g11432.t53.exon2 16198111 16198353
chr_1 g11432 g11432.t53 cds g11432.t53.CDS2 16198111 16198353
chr_1 g11432 g11432.t53 exon g11432.t53.exon3 16199164 16199299
chr_1 g11432 g11432.t53 cds g11432.t53.CDS3 16199164 16199299
chr_1 g11432 g11432.t53 exon g11432.t53.exon4 16200820 16200849
chr_1 g11432 g11432.t53 cds g11432.t53.CDS4 16200820 16200849
chr_1 g11432 g11432.t53 TSS g11432.t53 16201105 16201105

Sequences

>g11432.t53 Gene=g11432 Length=438
ATGGTAATTATCTCACATTATTTTTATATTGAAGCATTCTCATTGTTCGACAAAGACGGT
GATGGCACAATTACCACAAAAGAATTGGGCACTGTGATGAGATCACTTGGTCAAAACCCG
ACAGAAGCTGAACTTCAGGATATGATTAACGAAGTTGATGCTGACGGCAATGGTACCATA
GATTTCCCTGAATTCTTAACTATGATGGCTCGCAAAATGAAAGATACTGATAGTGAAGAA
GAAATTCGGGAAGCATTCCGTGTATTTGATAAAGATGGCAATGGTTTCATCTCTGCAGCT
GAATTGCGCCACGTGATGACAAATTTGGGAGAAAAATTAACAGATGAAGAAGTCGATGAA
ATGATTCGTGAGGCAGATATTGATGGTGACGGACAAGTTAATTACGAAGAATTTGTCACC
ATGATGACATCAAAGTGA

>g11432.t53 Gene=g11432 Length=145
MVIISHYFYIEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTI
DFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDEEVDE
MIREADIDGDGQVNYEEFVTMMTSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11432.t53 CDD cd00051 EFh 11 70 4.31983E-21
9 g11432.t53 CDD cd00051 EFh 81 143 4.47683E-24
7 g11432.t53 Gene3D G3DSA:1.10.238.10 - 10 106 1.2E-68
6 g11432.t53 Gene3D G3DSA:1.10.238.10 - 107 143 2.5E-17
3 g11432.t53 PANTHER PTHR23050:SF401 CALMODULIN 9 145 1.4E-88
4 g11432.t53 PANTHER PTHR23050 CALCIUM BINDING PROTEIN 9 145 1.4E-88
2 g11432.t53 Pfam PF13499 EF-hand domain pair 11 69 5.5E-15
1 g11432.t53 Pfam PF13499 EF-hand domain pair 79 142 7.4E-19
11 g11432.t53 ProSitePatterns PS00018 EF-hand calcium-binding domain. 17 29 -
12 g11432.t53 ProSitePatterns PS00018 EF-hand calcium-binding domain. 53 65 -
10 g11432.t53 ProSitePatterns PS00018 EF-hand calcium-binding domain. 90 102 -
13 g11432.t53 ProSitePatterns PS00018 EF-hand calcium-binding domain. 126 138 -
19 g11432.t53 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 11 39 13.872
18 g11432.t53 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 40 75 14.792
21 g11432.t53 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 77 112 17.972
20 g11432.t53 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 113 145 15.155
16 g11432.t53 SMART SM00054 efh_1 8 36 1.7E-5
15 g11432.t53 SMART SM00054 efh_1 44 72 7.2E-9
17 g11432.t53 SMART SM00054 efh_1 81 109 5.8E-9
14 g11432.t53 SMART SM00054 efh_1 117 145 1.3E-9
5 g11432.t53 SUPERFAMILY SSF47473 EF-hand 9 144 2.12E-54

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005509 calcium ion binding MF
GO:0019722 calcium-mediated signaling BP

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed